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Building complex computer systems with RET logic, we first investigate the simple filtering provided by single chromophores and one of its potential applications---Network-on-Chip (NoC). We remove ring resonators from current nanophotonic NoC and introduce chromophores and Quantum Dot LED(QD_LED)to provide similar functions. However, these changes enable CNoC to be more energy efficient with smaller area compared to current nanophotonic NoC if proper topologies are chosen. Moreover, we can scale up to a 320X320 optical crossbar with CNoC. Preliminary Lab results demonstrate the feasibility of introducing chromophores into NoC. We also propose three methods to use RET logic to build complex computer systems: 1) Cascade multiple levels of RET logic without a non-linear gain media to provide limited functionality; 2) Design an Optical Logic Element (OLE) as a basic computing unit to support complete logic; 3) Use hidden Markov model or Neural network composed of chromophores to provide some complex functions. A SPICE model of OLE is built to evaluate its performance and simulation results show that OLE has 10X better Power-Delay Product(PDP) than current CMOS process.